Notations and conventions in molecular spectroscopy: part 1. General spectroscopic notation

The field of Molecular Spectroscopy was surveyed in order to determine a set of conventions and symbols which are in common use in the spectroscopic literature. This document, which is Part I in a series, establishes the notations and conventions used for general spectroscopic notations and deals with quantum mechanics, quantum numbers (vibrational states, angular momentum and energy levels), spectroscopic transitions, and miscellaneous notations (e.g. spectroscopic terms). Further parts will follow, dealing inter alia with symmetry notation, permutation and permutation-inversion symmetry notation, vibration-rotation spectroscopy and electronic spectroscopy

Notations and conventions in molecular spectroscopy: part 2. Symmetry notation

The field of Molecular Spectroscopy was surveyed in order to determine a set of conventions and symbols which are in common use in the spectroscopic literature. This document, which is Part 2 in a series, establishes the notations and conventions used for the description of symmetry in rigid molecules, using the Schoenflies notation. It deals firstly with the symmetry operators of the molecular point groups (also drawing attention to the difference between symmetry operators and elements). The conventions and notations of the molecular point groups are then established, followed by those of the representations of these groups as used in molecular spectroscopy. Further parts will follow, dealing inter alia with permutation and permutation-inversion symmetry notation, vibration-rotation spectroscopy and electronic spectroscopy

Infrared spectroscopy of HCOOH in interstellar ice analogues

Context: HCOOH is one of the more common species in interstellar ices with abundances of 1-5% with respect to solid H2O. Aims: This study aims at characterizing the HCOOH spectral features in astrophysically relevant ice mixtures in order to interpret astronomical data. Methods: The ices are grown under high vacuum conditions and spectra are recorded in transmission using a Fourier transform infrared spectrometer. Pure HCOOH ices deposited at 15 K and 145 K are studied, as well as binary and tertiary mixtures containing H2O, CO, CO2 and CH3OH. The mixture concentrations are varied from 50:50% to ~10:90% for HCOOH:H2O. Binary mixtures of HCOOH:X and tertiary mixtures of HCOOH:H2O:X with X = CO, CO2, and CH3OH, are studied for concentrations of ~10:90% and ~7:67:26%, respectively. Results: Pure HCOOH ice spectra show broad bands which split around 120 K due to the conversion of a dimer to a chain-structure. Broad single component bands are found for mixtures with H2O. Additional spectral components are present in mixtures with CO, CO2 and CH3OH. The resulting peak position, full width at half maximum and band strength depend strongly on ice structure, temperature, matrix constituents and the HCOOH concentration. Comparison of the solid HCOOH 5.9, 7.2, and 8.1 micron features with astronomical data toward the low mass source HH 46 and high mass source W 33A shows that spectra of binary mixtures do not reproduce the observed ice features. However, our tertiary mixtures especially with CH3OH match the astronomical data very well. Thus interstellar HCOOH is most likely present in tertiary or more complex mixtures with H2O, CH3OH and potentially also CO or CO2, providing constraints on its formation.Comment: 11 pages, 10 figures, accepted by A&

Ices in the edge-on disk CRBR 2422.8-3423: Spitzer spectroscopy and Monte Carlo radiative transfer modeling

We present 5.2-37.2 micron spectroscopy of the edge-on circumstellar disk CRBR 2422.8-3423 obtained using the InfraRed Spectrograph (IRS) of the Spitzer Space Telescope. The IRS spectrum is combined with ground-based 3-5 micron spectroscopy to obtain a complete inventory of solid state material present along the line of sight toward the source. We model the object with a 2D axisymmetric (effectively 3D) Monte Carlo radiative transfer code. It is found that the model disk, assuming a standard flaring structure, is too warm to contain the very large observed column density of pure CO ice, but is possibly responsible for up to 50% of the water, CO2 and minor ice species. In particular the 6.85 micron band, tentatively due to NH4+, exhibits a prominent red wing, indicating a significant contribution from warm ice in the disk. It is argued that the pure CO ice is located in the dense core Oph-F in front of the source seen in the submillimeter imaging, with the CO gas in the core highly depleted. The model is used to predict which circumstances are most favourable for direct observations of ices in edge-on circumstellar disks. Ice bands will in general be deepest for inclinations similar to the disk opening angle, i.e. ~70 degrees. Due to the high optical depths of typical disk mid-planes, ice absorption bands will often probe warmer ice located in the upper layers of nearly edge-on disks. The ratios between different ice bands are found to vary by up to an order of magnitude depending on disk inclination due to radiative transfer effects caused by the 2D structure of the disk. Ratios between ice bands of the same species can therefore be used to constrain the location of the ices in a circumstellar disk. [Abstract abridged]Comment: 49 pages, accepted for publication in Ap

Methanol Masers as Tracers of Circumstellar Disks

We show that in many methanol maser sources the masers are located in lines, with a velocity gradient along them which suggests that the masers are situated in edge-on circumstellar, or protoplanetary, disks. We present VLBI observations of the methanol maser source G309.92+0.48, in the 12.2 GHz transition, which confirm previous observations that the masers in this source lie along a line. We show that such sources are not only linear in space but, in many cases, also have a linear velocity gradient. We then model these and other data in both the 6.7 GHz and the 12.2 GHz transition from a number of star formation regions, and show that the observed spatial and velocity distribution of methanol masers, and the derived Keplerian masses, are consistent with a circumstellar disk rotating around an OB star. We consider this and other hypotheses, and conclude that about half of these methanol masers are probably located in edge-on circumstellar disks around young stars. This is of particular significance for studies of circumstellar disks because of the detailed velocity information available from the masers.Comment: 38 pages, 13 figures accepted by Ap

Interaction between IRF6 and TGFA Genes Contribute to the Risk of Nonsyndromic Cleft Lip/Palate

Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10-6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10-6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10-6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans. © 2012 Letra et al

Complex molecules in the hot core of the low mass protostar NGC1333-IRAS4A

We report the detection of complex molecules (HCOOCH_3, HCOOH and CH_3CN), signposts of a "hot core" like region, toward the low mass, Class 0 source NGC1333-IRAS4A. This is the second low mass protostar where such complex molecules have been searched for and reported, the other source being IRAS16293-2422. It is therefore likely that compact (few tens of AUs) regions of dense and warm gas, where the chemistry is dominated by the evaporation of grain mantles, and where complex molecules are found, are common in low mass Class 0 sources.Given that the chemical formation timescale is much shorter than the gas hot core crossing time, it is not clear whether the reported complex molecules are formed on the grain surfaces (first generation molecules) or in the warm gas by reactions involving the evaporated mantle constituents (second generation molecules). We do not find evidence for large differences in the molecular abundances, normalized to the formaldehyde abundance, between the two solar type protostars, suggesting perhaps a common origin.Comment: 13 pages, 3 figures; accepted by Ap

Effects of CO2 on H2O band profiles and band strengths in mixed H2O:CO2 ices

H2O is the most abundant component of astrophysical ices. In most lines of sight it is not possible to fit both the H2O 3 um stretching, the 6 um bending and the 13 um libration band intensities with a single pure H2O spectrum. Recent Spitzer observations have revealed CO2 ice in high abundances and it has been suggested that CO2 mixed into H2O ice can affect relative strengths of the 3 um and 6 um bands. We used laboratory infrared transmission spectroscopy of H2O:CO2 ice mixtures to investigate the effects of CO2 on H2O ice spectral features at 15-135 K. We find that the H2O peak profiles and band strengths are significantly different in H2O:CO2 ice mixtures compared to pure H2O ice. In all H2O:CO2 mixtures, a strong free-OH stretching band appears around 2.73 um, which can be used to put an upper limit on the CO2 concentration in the H2O ice. The H2O bending mode profile also changes drastically with CO2 concentration; the broad pure H2O band gives way to two narrow bands as the CO2 concentration is increased. This makes it crucial to constrain the environment of H2O ice to enable correct assignments of other species contributing to the interstellar 6 um absorption band. The amount of CO2 present in the H2O ice of B5:IRS1 is estimated by simultaneously comparing the H2O stretching and bending regions and the CO2 bending mode to laboratory spectra of H2O, CO2, H2O:CO2 and HCOOH.Comment: 12 pages, 11 figures, accepted by A&